|
| Status |
Public on Apr 20, 2022 |
| Title |
Adult_BNST_Female_E2_3 |
| Sample type |
SRA |
| |
|
| Source name |
Bed nucleus of the stria terminalis, posterior
|
| Organism |
Mus musculus |
| Characteristics |
age: 10-12 weeks old
tissue: BNSTp
Sex: Female
treatment: Estradiol
|
| Treatment protocol |
Animals were injected subcutaneously with 5 ug estradiol benzoate or vehicle control (corn oil) 4 hours prior to brain dissection.
|
| Growth protocol |
8-12 week-old Esr1Cre/+;Rpl22-HA/+ females or males were gonadectomized to clear circulating hormones. 3 weeks post-gonadectomy, females or males were treated for 4 hr.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Microdissected tissue from 8-9 mice was pooled and frozen at -80oC for each sample. Tissue homogenization, immunoprecipitation of polysomes from Esr1+ neurons, and mRNA extraction was performed as previously described (Heiman et al., 2014; Sanz et al., 2009).
Libraries were prepared according to instructions provided by NuGEN Ovation RNA-Seq kits (7102 and 0344).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNASeq_BNST.xls
|
| Data processing |
For adult dataset, reads were adapter trimmed and quality filtered (q>30) using the Fast-X toolkit (http://hannonlab.cshl.edu/fastx_toolkit). For neonatal dataset, reads were adapter trimmed and quality filtered (q>30) using cutadapt.
Filtered reads were mapped to the mm10 reference genome using STAR.
The number of reads mapped to each gene (exons only) was calculated using featureCounts. For the neonatal dataset, technical duplicate reads were removed using the manufacturer's nudup.py script (https://github.com/tecangenomics/nudup). The number of reads mapping to each gene (including introns) was calculated using featureCounts.
Differential expression analysis was performed with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content:
RNASeq_BNST: xls file with differential expression results and read counts for all samples.
Neonatal_BNST: xlsx file with differential expression results and read counts for all samples.
|
| |
|
| Submission date |
Feb 04, 2020 |
| Last update date |
Apr 20, 2022 |
| Contact name |
Melody Wu |
| E-mail(s) |
mwu@cshl.edu
|
| Organization name |
Cold Spring Harbor Laboratory
|
| Street address |
1 Bungtown Rd
|
| City |
Cold Spring Harbor |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE144717 |
Gene regulation by gonadal hormone receptors defines brain sex differences-[RNA-Seq] |
| GSE144718 |
Gene regulation by gonadal hormone receptors defines brain sex differences |
|
| Relations |
| BioSample |
SAMN13981929 |
| SRA |
SRX7671754 |
